19-54220579-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006864.4(LILRB3):c.1207A>T(p.Asn403Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,437,074 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 8/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N403D) has been classified as Uncertain significance.
Frequency
Consequence
NM_006864.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LILRB3 | NM_006864.4 | c.1207A>T | p.Asn403Tyr | missense_variant | 6/13 | ENST00000445347.2 | |
LOC124904768 | XR_007067339.1 | n.710+975T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LILRB3 | ENST00000445347.2 | c.1207A>T | p.Asn403Tyr | missense_variant | 6/13 | 2 | NM_006864.4 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000354 AC: 4AN: 112846Hom.: 2 Cov.: 19
GnomAD4 exome AF: 0.0000151 AC: 20AN: 1324228Hom.: 3 Cov.: 43 AF XY: 0.00000907 AC XY: 6AN XY: 661182
GnomAD4 genome ? AF: 0.0000354 AC: 4AN: 112846Hom.: 2 Cov.: 19 AF XY: 0.0000733 AC XY: 4AN XY: 54542
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.1207A>T (p.N403Y) alteration is located in exon 6 (coding exon 6) of the LILRB3 gene. This alteration results from a A to T substitution at nucleotide position 1207, causing the asparagine (N) at amino acid position 403 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at